Rat Genomics PDF
Preview Rat Genomics
Methods in Molecular Biology 2018 G. Thomas Hayman Jennifer R. Smith Melinda R. Dwinell Mary Shimoyama Editors Rat Genomics M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences University ofHertfordshire Hatfield, Hertfordshire, UK Forfurther volumes: http://www.springer.com/series/7651 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. Rat Genomics Edited by G. Thomas Hayman Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA Jennifer R. Smith Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA Melinda R. Dwinell Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA Department of Physiology, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA Mary Shimoyama Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA Editors G.ThomasHayman JenniferR.Smith DepartmentofBiomedicalEngineering DepartmentofBiomedicalEngineering RatGenomeDatabase RatGenomeDatabase MedicalCollegeofWisconsin MedicalCollegeofWisconsin Milwaukee,WI,USA Milwaukee,WI,USA MelindaR.Dwinell MaryShimoyama GenomicSciencesandPrecision DepartmentofBiomedicalEngineering MedicineCenter RatGenomeDatabase MedicalCollegeofWisconsin MedicalCollegeofWisconsin Milwaukee,WI,USA Milwaukee,WI,USA DepartmentofPhysiology RatGenomeDatabase MedicalCollegeofWisconsin Milwaukee,WI,USA ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-4939-9580-6 ISBN978-1-4939-9581-3 (eBook) https://doi.org/10.1007/978-1-4939-9581-3 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeenmade. Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:233SpringStreet,NewYork,NY10013,U.S.A. Dedication This book is gratefully dedicated to the rat research community and to colleagues and friends who are gone too soon: Rat Genome Database members, Dr. Timothy F. Lowry and Dr. Victoria Petri, and founder of the Rat Resource and Research Center, Dr. John K.Critser.Theyaresincerelymissed. v Preface It is an exciting time to be involved in rat research. The rich history of physiological and behavioral data that is available for the rat spans over 150 years of research. This extensive bodyofdataprovidesasolidfoundationfortheuseofgenomictechnologiessuchaswhole- genome and whole-exome sequencing, single-nucleotide variant discovery, and transcrip- tomics to explore similarities and differences between established rat models for human diseasessuchaskidneydisease,cancer,andmetabolicsyndrome,aswellasnewmodelslike the hybrid rat diversity panel. Recent advances in the use of genome-editing reagents and embryonic stem cells now allow researchers to produce new, more targeted models and to discoverthemolecularmechanismsunderlyingbothnormalanddisease-relatedphysiologi- cal processes. Thanks to the improvements in cryopreservation and rederivation, new models can be produced, studied for a period of time, and then preserved and stored to awaitnewquestionsortheadventofnewtechnologiestouncovertheanswerstoquestions we can’t answer now and, in some cases, don’t even know we should be asking. The emergingareasofinterest,suchasthemicrobiome,haveopenedupnewvistasforresearch- ersinterestedintheinteractionsbetweengeneticsandtheenvironment. This book provides both a historical perspective on rat research through the years and practicalinformationtosupportresearcherseithercurrentlyinvolvedingenomicresearchor planning to begin such a project. In some cases, a detailed protocol is provided for researcherslookingtomoveintoanewareaofinvestigationortoleverageanewtechnology. Inothercases,adetailedreviewoftheexistingmodelsoradescriptionofavailableresources can help the researcherfind, understand, and/or utilize the information, the data, and the tools that they need to support their research efforts. Whatever the application, it is becoming increasingly obvious that in this so-called post-genomic era, no single type of research is sufficient to answer the increasingly complex questions of human disease and translationalresearch.Theratasabiomedicalmodelisuniquelypoisedtoprovidetheideal combinationofestablishedexperimentalmodels,extensivephysiologicaldata,andgenomic manipulabilitytofacilitateexplorationoftheunderlyingbiology. Milwaukee,WI,USA JenniferR.Smith vii Acknowledgments We are thankful for nearly 20 years of funding from the National Heart, Lung, and Blood InstituteonbehalfoftheNationalInstitutesofHealth.Weappreciatethecontributionsof the authors and the assistance of Prof. John Walker and Ms. Anna Rakovsky, which helped makethisbookareality. ix Contents Dedication.................................................................. v Preface ..................................................................... vii Acknowledgments............................................................. ix Contributors................................................................. xiii 1 TheRat:AModelUsedinBiomedicalResearch............................ 1 JenniferR.Smith,ElizabethR.Bolton,andMelindaR.Dwinell 2 RatGenomeAssemblies,Annotation,andVariantRepository ................ 43 MonikaTutaj,JenniferR.Smith,andElizabethR.Bolton 3 RatGenomeDatabases,Repositories,andTools............................ 71 StanleyJ.F.Laulederkind,G.ThomasHayman,Shur-JenWang, MatthewJ.Hoffman,JenniferR.Smith,ElizabethR.Bolton, JeffDePons,MarekA.Tutaj,MonikaTutaj,JyothiThota, MelindaR.Dwinell,andMaryShimoyama 4 NextGenerationTransgenicRatModelProduction......................... 97 WandaE.Filipiak,ElizabethD.Hughes,GalinaB.Gavrilina, AnnaK.LaForest,andThomasL.Saunders 5 EmbryonicStemCellsandGeneManipulationinRat....................... 115 MasumiHirabayashi,AkikoTakizawa,andShinichiHochi 6 ProtocolsforCryopreservationandRederivationofRatGametes............. 131 AkikoTakizawaandTomooEto 7 FluorescentImagingandMicroscopyforDynamicProcessesinRats .......... 151 RubenM.Sandoval,BruceA.Molitoris,andOlegPalygin 8 LibraryPreparationforMultiplexedReducedRepresentation BisulfiteSequencingwithaUniversalAdapter.............................. 177 YongLiu,AlisonJ.Kriegel,andMingyuLiang 9 CharacterizationoftheRatGutMicrobiotavia16SrRNA AmpliconLibrarySequencing ............................................ 195 AaronC.Ericsson,SusheelB.Busi,andJamesM.Amos-Landgraf 10 NetworkinginBiology:TheHybridRatDiversityPanel..................... 213 BorisTabakoff,HarrySmith,Lauren A.Vanderlinden, PaulaL.Hoffman,andLauraM.Saba 11 UsingHeterogeneousStocksforFine-MappingGenetically ComplexTraits......................................................... 233 LeahC.SolbergWoodsandAbrahamA.Palmer 12 MappingMammaryTumorTraitsintheRat............................... 249 MichaelJ.Flister,AmitJoshi,CarmenBergom, andHallgeirRui 13 RatModelsofMetabolicSyndrome....................................... 269 AnneE.Kwitek xi xii Contents 14 GenomicResearchinRatModelsofKidneyDisease ........................ 287 YoramYagil,RonenLevi-Varadi,andChanaYagil 15 RatModelsofExercisefor theStudyofComplexDisease ................... 309 Lauren GerardKochandStevenL.Britton 16 BehavioralGeneticStudiesinRats ........................................ 319 YangsuRenandAbrahamA.Palmer Index ...................................................................... 327
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